The fact that you cannot explore a ruin that the Mykara have claimed is a good game mechanic, creates tension between the different factions. One faction wants to explore, the other faction wants to grow, its great.

However, I've made an alliance with the Mykara and still cannot explore the ruins. I don't want to break our alliance, and why wouldn't I be able to?

I believe that if a faction is allied with the Mykara they should be able to explore the ruins without destroying the fungal blooms to do it.

I also believe that the Mykara should be able to build fungal blooms on ruins (but not minor faction villages) in allied territory.

And I believe that the Mykara and their Allies should get a special technology that if they both research (and research can be traded!) then they can use the Mykara's network to teleport the same way the Mykara can.

This would create some interesting alliance options for players and make it desirable to ally with the Mykara for at least some players.

As it is right now, I usually just wipe the Mykara out early because they take over all the ruins and it is so annoying. And it is particularly annoying as the Roaming Clans who can't declare war against the Mykara. Sure, you can annoy them enough that they will eventually declare war on you, but I don't even want that to happen as Roming Clans. I feel like I should be able to win peacefully without destroying the Mykara or their blooms, and without it being such a drawback to try and do so.

I fully agree with you on that one. that is one of the reasons why i do not play them when i do a multi game with my friends. (sadly, as i quite like playing them)